OpenSourceMalaria

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (added charman group to collaborators)
(Current Projects)
(8 intermediate revisions not shown.)
Line 11: Line 11:
There are lots of things needed, but the main thing is experimental input. If you're a scientist with access to a lab, open source drug discovery needs you. If you want to know what open source drug discovery is, go [[OSDD:Huh%3F|here]]. For anyone new to the project here is a [[short guide to using the Electronic Lab Notebook]].
There are lots of things needed, but the main thing is experimental input. If you're a scientist with access to a lab, open source drug discovery needs you. If you want to know what open source drug discovery is, go [[OSDD:Huh%3F|here]]. For anyone new to the project here is a [[short guide to using the Electronic Lab Notebook]].
-
Currently there are three active projects on-going:
+
A summary of our efforts to date can be found in [[OSDDMalaria:GSK Arylpyrrole Series:Story so far|The Story So Far]].
-
* [[OSDDMalaria:GSK_Arylpyrrole_Series|GSK arylpyrrole series]] - plus a [[OSDDMalaria:GSK Arylpyrrole Series:Story so far|human-readable summary]] of the current project status.
+
Currently there are three active [[OSDDMalaria:Projects|projects]] on-going:
 +
 
 +
* [[OSDDMalaria:GSK_Arylpyrrole_Series|GSK arylpyrrole series]]  
* [[OSDDMalaria:GSK_Triazolourea_Singleton|GSK Triazolourea Singleton]]
* [[OSDDMalaria:GSK_Triazolourea_Singleton|GSK Triazolourea Singleton]]
* [[OSDDMalaria:GSK_Amino-thienopyrimidine_Series|GSK Amino-thienopyrimidine Series]]
* [[OSDDMalaria:GSK_Amino-thienopyrimidine_Series|GSK Amino-thienopyrimidine Series]]
-
 
-
Project entries will be listed at [[OSDDMalaria:Projects|link]] in above menu.
 
=== Current Participants ===
=== Current Participants ===
Line 34: Line 34:
* [http://www.openlabfoundation.org/gsk.aspx GSK Tres Cantos], Spain
* [http://www.openlabfoundation.org/gsk.aspx GSK Tres Cantos], Spain
* [http://www.monash.edu.au/research/profiles/profile.html?sid=2143&pid=3154 Charman Group], Monash University
* [http://www.monash.edu.au/research/profiles/profile.html?sid=2143&pid=3154 Charman Group], Monash University
 +
 +
==Open Source Drug Discovery More Generally==
 +
 +
A [http://openwetware.org/wiki/OSDDMalaria:OSDD_Malaria_Meeting_Sydney_2012 one-day meeting on open source drug discovery for malaria] was held in February 2012. General issues surrounding the feasibility of open source drug discovery were discussed, followed by more specific malaria-related ideas. These talks are gradually [http://www.youtube.com/playlist?list=PL84A4E62C3C72863D going up on YouTube] with [http://www.thesynapticleap.org/node/390 annotations], and they frame many of the relevant issues, for example the landscape of drug discovery in neglected diseases, and whether patents are necessary in drug discovery. An important message is that open ''source'' drug discovery is where anyone may participate in driving the research, which is different from a more general use of the word "open" where data are made freely available, but perhaps after a delay which essentially prevents participation by others.
 +
 +
==How We Run the Project==
 +
 +
The way the project is run is one of the novelties, though as with everything in this project nothing is static and advice is always welcome on improvements. Raw experimental data are recorded in an online, openly-readable [http://malaria.ourexperiment.org/ electronic lab notebook]. [http://www.thesynapticleap.org/malaria/community The Synaptic Leap] is being used to discuss ideas and results, as well as plan future work. The project's [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts Google+ page] is a light way to keep up with developments and discuss. The project's [https://twitter.com/#!/OSDDMalaria Twitter feed] is a broadcast mechanism for updates. LinkedIn as used in the past on another project as a way of connecting with relevant experts, but has not been used much so far in this project. A [http://openwetware.org/wiki/Open_Source_Drug_Discovery_-_Malaria wiki] (that includes this page) is used to host the current overall project status. Updates on the project's progress can also be found at our  [http://www.facebook.com/OSDDforMalaria Facebook page], and this also a place for interaction. If you wish to participate in this project, you can sign up to all these sites, and you would then be sent the Twitter/G+ passwords so you can used the same accounts.
 +
 +
==Why Take Part?==
 +
 +
What of motivations? Why would people want to contribute to this project? Partly to solve a problem. Partly to be involved with quality science that is open, and hence subject to the most brutal form of ongoing peer-review. Partly for academic credentials since regular peer-reviewed papers will come from the project. Partly to demonstrate competence publicly - open science is meritocratic and status-blind. Perhaps a mixture of all these things.
 +
 +
A competition is possible in the future, i.e. with a cash prize. Progress towards a very promising lead compound series has been rapid, but there is a long road to a compound that looks sufficiently promising that it moves towards clinical trials. There's a lot of tweaking needed, and perhaps even the move to another series. It is not obvious what will happen. It is certain the project will need a lot more input than it has received to date. A prize may increase traffic and input. The competition would be teamless, however, awarded based on performance of individuals within a group where everything is shared. Not sharing data or ideas leads to disqualification. Such a competition is difficult to judge, difficult to award, and hence almost certainly worth doing. More about this is [http://intermolecular.wordpress.com/2011/11/13/open-science-funding-government-grants-and-cash-incentives/ here].
 +
 +
==Ownership==
 +
 +
A final point - the project is open. Nobody owns it. Those people most active in the project lead it while they are active. If you wish to contribute, in any capacity, please do so. There is no need to "clear" anything with existing project members by email first. To date is has been very common for current participants to receive questions/suggestions from people by email, which is to be discouraged. In the development of Linux, the need for Linus Torvalds to approve everything caused a serious bottleneck, and the observation that "Linus doesn't scale". ''Nobody scales, but the team does''. So it's more efficient if all the project discussions are held publicly. Many people do not like this idea. In science the idea of "beta testing" something is alien. When data are released in science there is an expectation that the data are correct, and essentially finished. This project eschews this view. All data are released immediately, all discussions are public, anyone can participate.
== Discussion ==
== Discussion ==
Line 40: Line 58:
Relevant papers are available in the [http://www.mendeley.com/groups/1846251/osddmalaria/ Mendeley group], to which anyone can add.
Relevant papers are available in the [http://www.mendeley.com/groups/1846251/osddmalaria/ Mendeley group], to which anyone can add.
 +
 +
==Licence==
 +
 +
The project's licence unless otherwise stated is [http://creativecommons.org/licenses/by/3.0/ CC-BY-3.0] meaning you can use whatever you want for whatever purpose, provided you cite the project.

Revision as of 00:56, 1 November 2012

Malaria Home        OSM So Far        Compound Series        Links        Open Source Research Home        Tech Ops        FAQ       


A hub for global efforts in open source drug discovery for malaria. If you are interested in open source drug discovery and would like to do something to combat malaria, then:

  • Get an OpenWetWare account
  • Edit this and other pages.
  • Contribute to current projects (below) or even start new ones!

Contents

Current Projects

There are lots of things needed, but the main thing is experimental input. If you're a scientist with access to a lab, open source drug discovery needs you. If you want to know what open source drug discovery is, go here. For anyone new to the project here is a short guide to using the Electronic Lab Notebook.

A summary of our efforts to date can be found in The Story So Far.

Currently there are three active projects on-going:

Current Participants

Medicinal Chemistry

Biology

Open Source Drug Discovery More Generally

A one-day meeting on open source drug discovery for malaria was held in February 2012. General issues surrounding the feasibility of open source drug discovery were discussed, followed by more specific malaria-related ideas. These talks are gradually going up on YouTube with annotations, and they frame many of the relevant issues, for example the landscape of drug discovery in neglected diseases, and whether patents are necessary in drug discovery. An important message is that open source drug discovery is where anyone may participate in driving the research, which is different from a more general use of the word "open" where data are made freely available, but perhaps after a delay which essentially prevents participation by others.

How We Run the Project

The way the project is run is one of the novelties, though as with everything in this project nothing is static and advice is always welcome on improvements. Raw experimental data are recorded in an online, openly-readable electronic lab notebook. The Synaptic Leap is being used to discuss ideas and results, as well as plan future work. The project's Google+ page is a light way to keep up with developments and discuss. The project's Twitter feed is a broadcast mechanism for updates. LinkedIn as used in the past on another project as a way of connecting with relevant experts, but has not been used much so far in this project. A wiki (that includes this page) is used to host the current overall project status. Updates on the project's progress can also be found at our Facebook page, and this also a place for interaction. If you wish to participate in this project, you can sign up to all these sites, and you would then be sent the Twitter/G+ passwords so you can used the same accounts.

Why Take Part?

What of motivations? Why would people want to contribute to this project? Partly to solve a problem. Partly to be involved with quality science that is open, and hence subject to the most brutal form of ongoing peer-review. Partly for academic credentials since regular peer-reviewed papers will come from the project. Partly to demonstrate competence publicly - open science is meritocratic and status-blind. Perhaps a mixture of all these things.

A competition is possible in the future, i.e. with a cash prize. Progress towards a very promising lead compound series has been rapid, but there is a long road to a compound that looks sufficiently promising that it moves towards clinical trials. There's a lot of tweaking needed, and perhaps even the move to another series. It is not obvious what will happen. It is certain the project will need a lot more input than it has received to date. A prize may increase traffic and input. The competition would be teamless, however, awarded based on performance of individuals within a group where everything is shared. Not sharing data or ideas leads to disqualification. Such a competition is difficult to judge, difficult to award, and hence almost certainly worth doing. More about this is here.

Ownership

A final point - the project is open. Nobody owns it. Those people most active in the project lead it while they are active. If you wish to contribute, in any capacity, please do so. There is no need to "clear" anything with existing project members by email first. To date is has been very common for current participants to receive questions/suggestions from people by email, which is to be discouraged. In the development of Linux, the need for Linus Torvalds to approve everything caused a serious bottleneck, and the observation that "Linus doesn't scale". Nobody scales, but the team does. So it's more efficient if all the project discussions are held publicly. Many people do not like this idea. In science the idea of "beta testing" something is alien. When data are released in science there is an expectation that the data are correct, and essentially finished. This project eschews this view. All data are released immediately, all discussions are public, anyone can participate.

Discussion

This is a wiki, meaning it's meant as a site for how projects are going. For discussion try The Synaptic Leap, or the project's Google+ page, and for updates try the Twitter feed and Facebook Page. If you would like access to the Twitter or G+ accounts because you've become a member of the project please email OSDD.Malaria@gmail.com.

Relevant papers are available in the Mendeley group, to which anyone can add.

Licence

The project's licence unless otherwise stated is CC-BY-3.0 meaning you can use whatever you want for whatever purpose, provided you cite the project.

Personal tools